The guy who got kicked out was elected. The guy who seized power took over via a military coup.
The African Union and the US have also condemned the coup. If the EU had some sneaky, nefarious scheme to have a "puppet" in place, why would they be objecting to the coup?
That's fine but you'd think the money was supposed to be used to improve the lives of the people and not to line the pockets of the ruling party/clique